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- PDB-1al5: A-TRACT RNA DODECAMER, NMR, 12 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1al5
TitleA-TRACT RNA DODECAMER, NMR, 12 STRUCTURES
ComponentsRNA (5'-R(*CP*GP*CP*AP*AP*AP*UP*UP*UP*GP*CP*G)-3')
KeywordsRNA / RNA DUPLEX / RIBONUCLEIC ACID
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / DIRECT REFINEMENT, RMD
AuthorsConte, M.R. / Conn, G.L. / Brown, T. / Lane, A.N.
Citation
Journal: Nucleic Acids Res. / Year: 1997
Title: Conformational properties and thermodynamics of the RNA duplex r(CGCAAAUUUGCG)2: comparison with the DNA analogue d(CGCAAATTTGCG)2.
Authors: Conte, M.R. / Conn, G.L. / Brown, T. / Lane, A.N.
#1: Journal: Nucleic Acids Res. / Year: 1996
Title: Hydration of the RNA Duplex R(Cgcaaauuugcg)2 Determined by NMR
Authors: Conte, M.R. / Conn, G.L. / Brown, T. / Lane, A.N.
History
DepositionJun 11, 1997Processing site: BNL
Revision 1.0Dec 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: ndb_struct_na_base_pair / pdbx_database_status ...ndb_struct_na_base_pair / pdbx_database_status / pdbx_entity_src_syn / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _ndb_struct_na_base_pair.opening / _pdbx_database_status.process_site ..._ndb_struct_na_base_pair.opening / _pdbx_database_status.process_site / _pdbx_nmr_software.authors / _pdbx_nmr_spectrometer.field_strength
Revision 1.4Nov 3, 2021Group: Data collection / Database references
Category: database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*CP*GP*CP*AP*AP*AP*UP*UP*UP*GP*CP*G)-3')
B: RNA (5'-R(*CP*GP*CP*AP*AP*AP*UP*UP*UP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,6252
Polymers7,6252
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1170 Å2
ΔGint-3 kcal/mol
Surface area4610 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)12 / 40MINIMAL RESTRAINT VIOLATIONS, LOW ENERGY, GOOD STEREOCHEMISTRY
Representative

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Components

#1: RNA chain RNA (5'-R(*CP*GP*CP*AP*AP*AP*UP*UP*UP*GP*CP*G)-3') / A-TRACT RNA


Mass: 3812.320 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
131H-INADEQUATE
14131P

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Sample preparation

Sample conditionspH: 7 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMBrukerAM4001
Varian UNITYPLUSVarianUNITYPLUS5002
Varian UNITYVarianUNITY6003

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Processing

NMR software
NameDeveloperClassification
DiscoverBIOSYMrefinement
DiscoverBIOSYMstructure calculation
NUCFITLanestructure calculation
RefinementMethod: DIRECT REFINEMENT, RMD / Software ordinal: 1 / Details: SEE REFERENCES FOR DETAILS.
NMR ensembleConformer selection criteria: MINIMAL RESTRAINT VIOLATIONS, LOW ENERGY, GOOD STEREOCHEMISTRY
Conformers calculated total number: 40 / Conformers submitted total number: 12

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